Comments (4)
And another questions:
how could i manually set the cpu and cores the muslce used.
muscle 5.1.linux64 [] 65.6Gb RAM, 40 cores
this is prettty huge of 65.6Gb
and 40 cores
.
Thanks
from muscle.
-
Muscle v5 only supports FASTA and EFA output formats, you need to use a third-party tool to convert formats.
-
That line reports the amount of RAM and CPU cores available, not the number actually used, this will be shown later as the command progresses. You can use the
-threads N
option to set a maximum number of cores.
from muscle.
- That line reports the amount of RAM and CPU cores available, not the number actually used, this will be shown later as the command progresses. You can use the
-threads N
option to set a maximum number of cores.
hi @rcedgar;
How can we limit the maximum amount of RAM used.
Today there was a program that spiked from 5G to 200G and then was killed and terminated.
Our compute nodes can't handle such a high memory spike.
Thanks so much.
from muscle.
Currently, muscle v5 does not provide command line options to specify the maximum amount of RAM. If you are using -align, then -super5 generally uses less RAM. By trying some examples, you can estimate roughly how much RAM will be used by your input data as a function of sequence length and number of sequences, then you can filter out datasets which are too big. Most cluster job managers and cloud services can set a maximum for a process.
from muscle.
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from muscle.